Reserve the first level headings (#) for the start of a new Module. This will help to organize your portfolio in an intuitive fashion.
Note: Please edit this template to your heart’s content. This is meant to be the armature upon which you build your individual portfolio. You do not need to keep this instructive text in your final portfolio, although you do need to keep module and assignment names so we can identify what is what.
The first of your second level headers (##) is to be used for the portfolio content checks. The Module 01 portfolio check has been built for you directly into this template, but will also be available as a stand-alone markdown document available on the MICB425 GitHub so that you know what is required in each module section in your portfolio. The completion status and comments will be filled in by the instructors during portfolio checks when your current portfolios are pulled from GitHub.
The remaining second level headers (##) are for separating data science Friday, regular course, and project content. In this module, you will only need to include data science Friday and regular course content; projects will come later in the course.
Third level headers (###) should be used for links to assignments, evidence worksheets, problem sets, and readings, as seen here.
Use this space to include your installation screenshots.
Detail the code you used to create, initialize, and push your portfolio repo to GitHub. This will be helpful as you will need to repeat many of these steps to update your porfolio throughout the course.
In Git: mkdir MICB425_portfolio cd MICB425_portfolio cd MICB425_portfolio Create repository on GitHub page. git init git add . git commit -m “First commit” git remote add origin https://remote_repository_URL git remote -v git push -u origin master
Paste your code from the in-class activity of recreating the example html.
The following assignment is an exercise for the reproduction of this .html document using the RStudio and RMarkdown tools we’ve shown you in class. Hopefully by the end of this, you won’t feel at all the way this poor PhD student does. We’re here to help, and when it comes to R, the internet is a really valuable resource. This open-source program has all kinds of tutorials online.
http://phdcomics.com/ Comic posted 1-17-2018
The goal of this R Markdown html challenge is to give you an opportunity to play with a bunch of different RMarkdown formatting. Consider it a chance to flex your RMarkdown muscles. Your goal is to write your own RMarkdown that rebuilds this html document as close to the original as possible. So, yes, this means you get to copy my irreverant tone exactly in your own Markdowns. It’s a little window into my psyche. Enjoy =)
hint: go to the PhD Comics website to see if you can find the image above
If you can’t find the exact image, just find a comparable from the PhD Comics website and include it in your markdown
Let’s be honest, this header is a little arbitrary. But show me that you can reproduce headers with different levels please. This is a level 3 header, for your reference (you can most easily tell this from the table of contents).
Perhaps you’re already really confused by the whole markdown thing. Maybe you’re so confused that you’ve forgotton how to add. Never fear!A calculator R is here:
1231521+12341556280987
## [1] 1.234156e+13
Or maybe, after you’ve added those numbers, you feel like it’s about time for a table! I’m going to leave all the guts of the coding here so you can see how libraries (R packages) are loaded into R (more on that later). It’s not terribly pretty, but it hints at how R works and how you will use it in the future. The summary function used below is a nice data exploration function that you may use in thefuture.
library(knitr)
kable(summary(cars),caption="I made this table with kable in the knitr package library")
| speed | dist | |
|---|---|---|
| Min. : 4.0 | Min. : 2.00 | |
| 1st Qu.:12.0 | 1st Qu.: 26.00 | |
| Median :15.0 | Median : 36.00 | |
| Mean :15.4 | Mean : 42.98 | |
| 3rd Qu.:19.0 | 3rd Qu.: 56.00 | |
| Max. :25.0 | Max. :120.00 |
And now you’ve almost finished your first RMarkdown! Feeling excited? We are! In fact, we’re so excited that maybe we need a big finale eh?
Here’s ours! Include a fun gif of your choice!
Silicon Valley
The template for the first Evidence Worksheet has been included here. The first thing for any assignment should link(s) to any relevant literature (which should be included as full citations in a module references section below).
You can copy-paste in the answers you recorded when working through the evidence worksheet into this portfolio template.
As you include Evidence worksheets and Problem sets in the future, ensure that you delineate Questions/Learning Objectives/etc. by using headers that are 4th level and greater. This will still create header markings when you render (knit) the document, but will exclude these levels from the Table of Contents. That’s a good thing. You don’t’ want to clutter the Table of Contents too much.
Describe the numerical abundance of microbial life in relation to ecology and biogeochemistry of Earth systems.
What were the main questions being asked?
What is the abundance of prokaryotes on earth? What is the total amount of cellular carbon produced by these prokaryotes on earth?
Other Habitats: - animals - human: cell density of prokaryotes on the skin multiply by skin surface area - insects like termite by counting number of insect and number of prokaryotes in said insect - leaves: can be estimated by assuming a dense population and high leaf area index
- air: pre-calculated Carbon Content: - estimated from cell numbers in soil, aquatic systems, and the subsurface - cellular carbon is assumed to be one-half of dry weight for soil and subsurface - take average dry weight of prokaryotic cells multiple by number of cell - aquatic systems: assumed that average cellular carbon for sedimentary and planktonic prokaryotes to be 10 and 20 fg of C/cell respectively then multiple that with number of cells in aquatic systems
Comment on the emergence of microbial life and the evolution of Earth systems
Indicate the key events in the evolution of Earth systems at each approximate moment in the time series. If times need to be adjusted or added to the timeline to fully account for the development of Earth systems, please do so.
Formation of Earth
Moon was formed to give Earth spin & tilt, day & night cycles, seasons
oldest mineral found (zircon)
earliest evidence of life in zircon
iron rich sedimentary rocks
stromatolites (organosedimentary structures produced by microbial trappings, usually but not always photosynthetic)
Glaciation: Earth would have appeared brown
rock recognized as redbeds -> evidence for oxidation
end of Snowball Earth
Eukaryote emergence
1.3 billion years ago
Cambrian explosion
emergence of land plants
H. Sapiens appear
Describe the dominant physical and chemical characteristics of Earth systems at the following waypoints:
seawater chemistry controlled by volcanism
methanogenesis (early); Greenhouse effect because of CH4 and CO2
CO2 levels hundrends times higher than now
nitrogen concentration close to modern levels
higher oxygen levels
Describe the numerical abundance of microbial life in relation to the ecology and biogeochemistry of Earth systems.
What are the primary prokaryotic habitats on Earth and how do they vary with respect to their capacity to support life? Provide a breakdown of total cell abundance for each primary habitat from the tables provided in the text.
a. Aquatic : 1.18 x 10^29^
b. Soil: 2.556 x 10^29^
What is the estimated prokaryotic cell abundance in the upper 200 m of the ocean and what fraction of this biomass is represented by marine cyanobacterium including Prochlorococcus? What is the significance of this ratio with respect to carbon cycling in the ocean and the atmospheric composition of the Earth? 3.6 x 1028 cyanobacteria: 4x 104 cells/ml / 5 x 105 cells x 100 = 8%
Based on information provided in the text and your knowledge of geography what is the deepest habitat capable of supporting prokaryotic life? What is the primary limiting factor at this depth?
Since the temperature drop is 22 degrees drop per km so the deepest part that can support life is Mariana Trench 10.9km + plus an extra 5 km
Based on information provided in the text your knowledge of geography what is the highest habitat capable of supporting prokaryotic life? What is the primary limiting factor at this height?
22 km on top of the 8.8 km on Mt. Everest. A limiting factor at that height would be obtaining enough nutrients.
Based on estimates of prokaryotic habitat limitation, what is the vertical distance of the Earth’s biosphere measured in km?
22 + 8.8 + 10.9 + 5 = 46.7 km
How was annual cellular production of prokaryotes described in Table 7 column four determined? (Provide an example of the calculation)
- 3.6 x 1028 / 16 x 365 = 8.4 x 1029 - population size divided by turnover time per day times 365 days
Given the large population size and high mutation rate of prokaryotic cells, what are the implications with respect to genetic diversity and adaptive potential? Are point mutations the only way in which microbial genomes diversify and adapt?
Prokaryotes would have high genetic diversity and the ability to adapt quickly dude to their high mutation rate. Insertions and deletions are generally detrimental to a gene’s function since they shift the reading frame so point mutations tend to be the most common, but there’s potential for these type of mutations to promote genetic diversity.
What relationships can be inferred between prokaryotic abundance, diversity, and metabolic potential based on the information provided in the text?
High prokaryotic abundance encourages the diversification of metabolic capabilities in prokaryotes. There are more likely to be more mutations taking place in a larger population of prokaryotes that allow them to fully take advantage of their environment and compete for different resources.
Discuss the role of microbial diversity and formation of coupled metabolism in driving global biogeochemical cycles.
abiotic processes are a source of nutrients for biotic reactions
result of a collective complex system made up of individual microbes
overcome thermodynamic barriers with synergistic cooperation of multispeicies assemblages
nitrous oxide is a potent greenhosue gass that contributes to global warming
microbes have core planetary gene set dispersed to them through vertical or horizontal gene transfer allow them to protect the metabolic pathway
Utilize this space to include a bibliography of any literature you want associated with this module. We recommend keeping this as the final header under each module.
An example for Whitman and Wiebe (1998) has been included below.
Whitman WB, Coleman DC, and Wiebe WJ. 1998. Prokaryotes: The unseen majority. Proc Natl Acad Sci USA. 95(12):6578–6583. PMC33863
Kasting JF, Siefert JL. 2002. Life and the evolution of earth â€TM s atmosphere. Library (Lond) 296:1066–1069.
Canfield DE, Glazer AN, Falkowski PG. 2010. The evolution and future of earth’s nitrogen cycle. Science (80- ) 330:192–196.
Falkowski PG, Fenchel T, Delong EF. 2008. The microbial engines that drive earth’s biogeochemical cycles. Science (80- ) 320:1034–1039.